2026-03-20 11:57
ftp://ftp.de.debian.org/debian/pool/main/b/blasr/blasr_5.3.5+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.8.0-106-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.70
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
cppcheck: head 2.20.0
head-info: 4412833 (2026-03-20 08:27:05 +0100)
count: 257 248
elapsed-time: 3.9 3.6
head-timing-info:

old-timing-info:

head results:
blasr-5.3.5/iblasr/MappingParameters.h:239:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/MappingParameters.h:403:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/MappingParameters.h:766:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGATIVE [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/MappingParameters.h:772:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HDFCCSONLY [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/ReadAlignments.hpp:110:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/ReadAlignments.hpp:149:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:120:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SMRTLogProbMatrix [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:439:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable length [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:464:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:551:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:612:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SMRTDistanceMatrix [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:940:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable StickPrint [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:1014:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:1057:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:1071:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:69:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:564:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Forward [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1272:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SMRTDistanceMatrix [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1417:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SMRTDistanceMatrix [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/RegisterFilterOptions.h:20:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGATIVE [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:38:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PositiveInteger [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:230:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:691:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:709:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
blasr-5.3.5/Blasr.cpp:190:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PBDATASET [valueFlowBailoutIncompleteVar]
blasr-5.3.5/Blasr.cpp:292:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PBDATASET [valueFlowBailoutIncompleteVar]
blasr-5.3.5/Blasr.cpp:570:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CCSDeNovo [valueFlowBailoutIncompleteVar]
blasr-5.3.5/Blasr.cpp:708:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
blasr-5.3.5/Blasr.cpp:831:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/iblasr/MappingParameters.h:770:28: style:inconclusive: Technically the member function 'MappingParameters::DetermineQueryReadType' can be const. [functionConst]
blasr-5.3.5/iblasr/ReadAlignments.hpp:67:28: style:inconclusive: Technically the member function 'ReadAlignments::GetNAlignedSeq' can be const. [functionConst]
blasr-5.3.5/iblasr/ReadAlignments.hpp:40:16: note: Technically the member function 'ReadAlignments::GetNAlignedSeq' can be const.
blasr-5.3.5/iblasr/ReadAlignments.hpp:67:28: note: Technically the member function 'ReadAlignments::GetNAlignedSeq' can be const.
blasr-5.3.5/iblasr/ReadAlignments.hpp:107:29: style:inconclusive: Technically the member function 'ReadAlignments::CheckSeqIndex' can be const. [functionConst]
blasr-5.3.5/iblasr/ReadAlignments.hpp:48:17: note: Technically the member function 'ReadAlignments::CheckSeqIndex' can be const.
blasr-5.3.5/iblasr/ReadAlignments.hpp:107:29: note: Technically the member function 'ReadAlignments::CheckSeqIndex' can be const.
blasr-5.3.5/iblasr/MappingIPC.h:46:10: style:inconclusive: Technically the member function 'MappingData < DNASuffixArray , FASTASequence , DNATuple >::ShallowCopySuffixArray' can be const. [functionConst]
blasr-5.3.5/iblasr/MappingIPC.h:60:10: style:inconclusive: Technically the member function 'MappingData < DNASuffixArray , FASTASequence , DNATuple >::ShallowCopySequenceIndexDatabase' can be const. [functionConst]
blasr-5.3.5/iblasr/MappingIPC.h:69:10: style:inconclusive: Technically the member function 'MappingData < DNASuffixArray , FASTASequence , DNATuple >::ShallowCopyTupleCountTable' can be const. [functionConst]
blasr-5.3.5/Blasr.cpp:579:14: style: Condition 'readIsCCS' is always true [knownConditionTrueFalse]
blasr-5.3.5/Blasr.cpp:562:19: note: Assuming that condition 'readIsCCS==false' is not redundant
blasr-5.3.5/Blasr.cpp:579:14: note: Condition 'readIsCCS' is always true
blasr-5.3.5/Blasr.cpp:1028:26: style: Condition 'params.useSuffixArray' is always true [knownConditionTrueFalse]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:942:44: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:943:33: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:958:41: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:959:30: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:839:27: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1241:45: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1242:33: style: C-style reference casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:38:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:60:44: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:62:39: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:63:44: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:64:47: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:65:49: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:66:39: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:73:27: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:76:27: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:181:52: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/Blasr.cpp:1407:32: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1466:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1466:67: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:118:54: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:121:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:155:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:298:20: style: Variable 'matchFound' is reassigned a value before the old one has been used. [redundantAssignment]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:23:20: note: matchFound is assigned
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:298:20: note: matchFound is overwritten
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:169:13: style: The scope of the variable 'alnStart' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:169:23: style: The scope of the variable 'alnEnd' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:339:9: style: The scope of the variable 'p' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:402:10: style: The scope of the variable 'overlapFound' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:512:9: style: The scope of the variable 'j' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:513:9: style: The scope of the variable 'numContained' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:514:9: style: The scope of the variable 'curNotContained' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:376:16: style: The scope of the variable 'clusterIndex' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:411:15: style: The scope of the variable 'minExpAnchors' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:419:13: style: The scope of the variable 'totalSignificantClusterSize' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:420:13: style: The scope of the variable 'maxClusterSize' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:424:13: style: The scope of the variable 'totalAnchorBases' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1281:9: style: The scope of the variable 'kbandScore' can be reduced. [variableScope]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1282:9: style: The scope of the variable 'qvAwareScore' can be reduced. [variableScope]
blasr-5.3.5/Blasr.cpp:253:34: style: Local variable 'smrtRead' shadows outer argument [shadowArgument]
blasr-5.3.5/Blasr.cpp:184:87: note: Shadowed declaration
blasr-5.3.5/Blasr.cpp:253:34: note: Shadow variable
blasr-5.3.5/Blasr.cpp:1114:19: style: Local variable 'outFilePtr' shadows outer variable [shadowVariable]
blasr-5.3.5/Blasr.cpp:19:15: note: Shadowed declaration
blasr-5.3.5/Blasr.cpp:1114:19: note: Shadow variable
blasr-5.3.5/iblasr/ReadAlignments.hpp:115:69: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:80:42: style: Parameter 'subreadInterval' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:80:78: style: Parameter 'params' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:108:34: style: Parameter 'smrtRead' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:132:54: style: Parameter 'subreads' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:46:68: style: Parameter 'alignmentPtrs' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:81:55: style: Parameter 'alignmentPtrs' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:95:82: style: Parameter 'params' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:335:75: style: Parameter 'params' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:431:54: style: Parameter 'params' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:506:52: style: Parameter 'params' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1394:69: style: Parameter 'subreadInterval' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/MappingIPC.h:86:91: style: Parameter 'paramsP' can be declared as reference to const [constParameterReference]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:120:30: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
blasr-5.3.5/iblasr/ReadAlignments.hpp:74:47: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:137:26: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/iblasr/BlasrMiscsImpl.hpp:168:61: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/Blasr.cpp:255:25: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/Blasr.cpp:427:69: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/Blasr.cpp:667:65: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/iblasr/RegisterFilterOptions.h:15:43: warning: Uninitialized variable: scoreSignInt [uninitvar]
blasr-5.3.5/iblasr/RegisterBlasrOptions.h:223:69: note: Calling function 'RegisterFilterOptions', 7th argument 'trashbinInt' value is <Uninit>
blasr-5.3.5/iblasr/RegisterFilterOptions.h:15:43: note: Uninitialized variable: scoreSignInt
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:238:33: style: Unused variable: nextIt [unusedVariable]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:402:23: style: Variable 'overlapFound' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrUtilsImpl.hpp:406:20: style: Variable 'setEnd' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:34:28: style: Variable 'numKeysMatched' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:43:34: style: Variable 'rcNumKeysMatched' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:48:28: style: Variable 'numKeysMatched' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:52:34: style: Variable 'rcNumKeysMatched' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:419:41: style: Variable 'totalSignificantClusterSize' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:424:30: style: Variable 'totalAnchorBases' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:443:53: style: Variable 'totalSignificantClusterSize' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:450:38: style: Variable 'totalAnchorBases' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/Blasr.cpp:1000:19: style: Unused variable: unalignedOutFile [unusedVariable]
blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1249:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
blasr-5.3.5/extrautils/BuildSequenceDB.cpp:35:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/BuildSequenceDB.cpp:26:19: style: Unused variable: fastaIn [unusedVariable]
blasr-5.3.5/extrautils/BwtToSuffixArray.cpp:14:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/BwtToSuffixArray.cpp:9:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/Evolve.cpp:57:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/Evolve.cpp:111:28: style: Condition 'it==maxIts' is always false [knownConditionTrueFalse]
blasr-5.3.5/extrautils/Evolve.cpp:108:26: note: Assignment 'it=0', assigned value is 0
blasr-5.3.5/extrautils/Evolve.cpp:111:28: note: Condition 'it==maxIts' is always false
blasr-5.3.5/extrautils/Evolve.cpp:93:15: style: The scope of the variable 'randomNumber' can be reduced. [variableScope]
blasr-5.3.5/extrautils/ExciseRepeats.cpp:11:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/ExciseRepeats.cpp:7:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/ExciseRepeats.cpp:25:19: style: Unused variable: seqOutFile [unusedVariable]
blasr-5.3.5/extrautils/PrintTupleCountTable.cpp:48:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/PrintTupleCountTable.cpp:35:30: style: The scope of the variable 'opts' can be reduced. [variableScope]
blasr-5.3.5/extrautils/SALS.cpp:12:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SALS.cpp:8:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/SAModify.cpp:14:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SAModify.cpp:47:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SAModify.cpp:35:9: style: The scope of the variable 'lcpLength' can be reduced. [variableScope]
blasr-5.3.5/extrautils/SAModify.cpp:19:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/SAModify.cpp:35:19: style: Variable 'lcpLength' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SAModify.cpp:36:24: style: Variable 'parsingOptions' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SAModify.cpp:44:23: style: Variable 'lcpLength' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SAModify.cpp:30:30: style: Unused variable: inFiles [unusedVariable]
blasr-5.3.5/extrautils/SWMatcher.cpp:17:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SWMatcher.cpp:38:9: style: The scope of the variable 'mismatch' can be reduced. [variableScope]
blasr-5.3.5/extrautils/SWMatcher.cpp:14:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/SWMatcher.cpp:34:9: style: Variable 'indelCost' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SimpleShredder.cpp:29:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PositiveInteger [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SimpleShredder.cpp:27:41: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/extrautils/SimpleShredder.cpp:76:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/extrautils/SimpleShredder.cpp:123:24: style: Variable 'gappedRead' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SimpleShredder.cpp:95:9: style: Variable 'maxRetry' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SimpleShredder.cpp:96:9: style: Variable 'retryNumber' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SimpleShredder.cpp:122:13: style: Unused variable: j [unusedVariable]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:68:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:16:5: warning:inconclusive: Member variable 'ScoredLength::score' is not initialized in the constructor. [uninitMemberVar]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:16:5: warning:inconclusive: Member variable 'ScoredLength::length' is not initialized in the constructor. [uninitMemberVar]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:131:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:133:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:230:29: style: Variable 'sample.type' is reassigned a value before the old one has been used. [redundantAssignment]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:219:25: note: sample.type is assigned
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:230:29: note: sample.type is overwritten
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:43:9: style: The scope of the variable 'minSamples' can be reduced. [variableScope]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:44:9: style: The scope of the variable 'maxSamples' can be reduced. [variableScope]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:39:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:155:53: performance: Searching before insertion is not necessary. Instead of 'maxLengthMap[nameStr]=ScoredLength(score,subreadLength)' consider using 'maxLengthMap.try_emplace(nameStr, ScoredLength(score,subreadLength));'. [stlFindInsert]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:54:9: style: Variable 'minAverageQual' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:79:9: style: Unused variable: fileNameIndex [unusedVariable]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:81:9: style: Variable 'numContextsReached' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/StoreQualityByContextFromCmpH5.cpp:82:9: style: Variable 'numContexts' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/extrautils/SuffixArrayToBWT.cpp:13:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/extrautils/SuffixArrayToBWT.cpp:10:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/utils/LoadPulses.cpp:67:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Standard [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:268:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:301:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BasField [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:400:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:428:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BasField [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:538:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Astro [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:681:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CCS [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:786:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:851:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:933:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:980:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:1064:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:1089:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:1565:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:1597:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:1687:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PositiveInteger [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/LoadPulses.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
blasr-5.3.5/utils/LoadPulses.cpp:2042:17: error: Unhandled exception thrown in function that is an entry point. [throwInEntryPoint]
blasr-5.3.5/utils/LoadPulses.cpp:775:14: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:775:48: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1132:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1146:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1158:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1170:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1183:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1196:40: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1524:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1528:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1532:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1536:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1541:36: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:1546:40: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:2215:22: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:2215:61: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/LoadPulses.cpp:111:73: style: Same expression 'fields[i]=="PulseWidth"' found multiple times in chain of '||' operators. [duplicateExpression]
blasr-5.3.5/utils/LoadPulses.cpp:1778:17: style: Variable 'useBaseFile' is reassigned a value before the old one has been used. [redundantAssignment]
blasr-5.3.5/utils/LoadPulses.cpp:1763:25: note: useBaseFile is assigned
blasr-5.3.5/utils/LoadPulses.cpp:1778:17: note: useBaseFile is overwritten
blasr-5.3.5/utils/LoadPulses.cpp:1562:17: style: The scope of the variable 'metric' can be reduced. [variableScope]
blasr-5.3.5/utils/LoadPulses.cpp:2189:23: style: The scope of the variable 'holeNumber' can be reduced. [variableScope]
blasr-5.3.5/utils/LoadPulses.cpp:2190:25: style: The scope of the variable 'readIndex' can be reduced. [variableScope]
blasr-5.3.5/utils/LoadPulses.cpp:2186:23: style: Local variable 'alignmentIndex' shadows outer variable [shadowVariable]
blasr-5.3.5/utils/LoadPulses.cpp:1914:10: note: Shadowed declaration
blasr-5.3.5/utils/LoadPulses.cpp:2186:23: note: Shadow variable
blasr-5.3.5/utils/LoadPulses.cpp:65:33: style: Parameter 'cmpFile' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:107:58: style: Parameter 'fields' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:293:48: style: Parameter 'requiredFields' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:442:54: style: Parameter 'metricsToLoad' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:445:34: style: Parameter 'totalAlnLength' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:641:36: style: Parameter 'baseFile' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:641:57: style: Parameter 'pulseFile' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:641:94: style: Parameter 'table' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:659:29: style: Parameter 'cmpFile' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:840:35: style: Variable 'lookupTable' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:934:20: style: Variable 'fieldType' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:981:20: style: Variable 'fieldType' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:1080:55: style: Parameter 'groupedLookupTablesIndexPairs' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/LoadPulses.cpp:2189:23: style: Variable 'holeNumber' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:2190:25: style: Variable 'readIndex' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:2191:23: style: Variable 'queryStart' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:2192:23: style: Variable 'queryEnd' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:2194:23: style: Variable 'offsetEnd' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/LoadPulses.cpp:512:93: error: Out of bounds access in expression 'byteAlignment[0]' because 'byteAlignment' is empty. [containerOutOfBounds]
blasr-5.3.5/utils/LoadPulses.cpp:503:31: note: Assuming condition is false
blasr-5.3.5/utils/LoadPulses.cpp:512:93: note: Access out of bounds
blasr-5.3.5/utils/LoadPulses.cpp:517:46: error: Out of bounds access in expression 'byteAlignment[0]' because 'byteAlignment' is empty. [containerOutOfBounds]
blasr-5.3.5/utils/LoadPulses.cpp:503:31: note: Assuming condition is false
blasr-5.3.5/utils/LoadPulses.cpp:517:46: note: Access out of bounds
blasr-5.3.5/utils/LoadPulses.cpp:517:89: error: Out of bounds access in expression 'alignedSequence[0]' because 'alignedSequence' is empty. [containerOutOfBounds]
blasr-5.3.5/utils/LoadPulses.cpp:503:31: note: Assuming condition is false
blasr-5.3.5/utils/LoadPulses.cpp:517:89: note: Access out of bounds
blasr-5.3.5/utils/LoadPulses.cpp:113:43: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/utils/LoadPulses.cpp:214:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/utils/LoadPulses.cpp:925:55: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/utils/LoadPulses.cpp:972:59: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
blasr-5.3.5/utils/LoadPulses.cpp:2361:57: style: Using fill with iterator 'readPulseIndexMetric.begin()' that is always empty. [knownEmptyContainer]
blasr-5.3.5/utils/LoadPulses.cpp:1105:27: style: Unused variable: startTimeOffsetMetric [unusedVariable]
blasr-5.3.5/utils/LoadPulses.cpp:2427:51: style: Variable 'qvMetric[qvMetric.size()-1]' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/utils/PulseToFasta.cpp:57:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PositiveInteger [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/PulseToFasta.cpp:289:37: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/PulseToFasta.cpp:291:22: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/PulseToFasta.cpp:302:30: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/SAWriter.cpp:16:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SAWriter.cpp:73:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable larsson [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SDPMatcher.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SDPMatcher.cpp:59:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Global [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SDPMatcher.cpp:145:30: style: Local variable 'scoreMat' shadows outer variable [shadowVariable]
blasr-5.3.5/utils/SDPMatcher.cpp:109:22: note: Shadowed declaration
blasr-5.3.5/utils/SDPMatcher.cpp:145:30: note: Shadow variable
blasr-5.3.5/utils/SDPMatcher.cpp:146:32: style: Local variable 'pathMat' shadows outer variable [shadowVariable]
blasr-5.3.5/utils/SDPMatcher.cpp:110:24: note: Shadowed declaration
blasr-5.3.5/utils/SDPMatcher.cpp:146:32: note: Shadow variable
blasr-5.3.5/utils/SDPMatcher.cpp:32:26: style: Parameter 'argv' can be declared as const array [constParameter]
blasr-5.3.5/utils/SDPMatcher.cpp:109:22: style: Unused variable: scoreMat [unusedVariable]
blasr-5.3.5/utils/SDPMatcher.cpp:110:24: style: Unused variable: pathMat [unusedVariable]
blasr-5.3.5/utils/SamFilter.cpp:89:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable qName [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamFilter.cpp:110:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamFilter.cpp:169:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamFilter.cpp:193:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamFilter.cpp:253:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INF_INT [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamFilter.cpp:84:58: style: Parameter 'allSAMAlignments' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/SamFilter.cpp:102:61: style: Parameter 'allSAMAlignments' can be declared as reference to const [constParameterReference]
blasr-5.3.5/utils/SamFilter.cpp:204:19: style: Variable 'entry' can be declared as reference to const [constVariableReference]
blasr-5.3.5/utils/SamFilter.cpp:366:17: style: Variable 'log' is assigned a value that is never used. [unreadVariable]
blasr-5.3.5/utils/SamToCmpH5.cpp:53:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PositiveInteger [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/SamToCmpH5.cpp:137:17: style: C-style pointer casting [cstyleCast]
blasr-5.3.5/utils/SamToM4.cpp:64:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/ToAfg.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/ToAfg.cpp:64:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
blasr-5.3.5/utils/ToAfg.cpp:29:26: style: Parameter 'argv' can be declared as const array [constParameter]
diff:
head blasr-5.3.5/iblasr/BlasrAlignImpl.hpp:1394:69: style: Parameter 'subreadInterval' can be declared as reference to const [constParameterReference]
head blasr-5.3.5/utils/LoadPulses.cpp:1080:55: style: Parameter 'groupedLookupTablesIndexPairs' can be declared as reference to const [constParameterReference]
head blasr-5.3.5/utils/LoadPulses.cpp:2189:23: style: Variable 'holeNumber' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:2190:25: style: Variable 'readIndex' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:2191:23: style: Variable 'queryStart' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:2192:23: style: Variable 'queryEnd' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:2194:23: style: Variable 'offsetEnd' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:934:20: style: Variable 'fieldType' can be declared as reference to const [constVariableReference]
head blasr-5.3.5/utils/LoadPulses.cpp:981:20: style: Variable 'fieldType' can be declared as reference to const [constVariableReference]


DONE